Sequence
atgc intronic sequence ATGC exonic sequencegtgggcagccagtcatacttgattatttttcttgttcgtgtacttgatcgttatttccccgattattagttttaacttgttccaatatcgagcagGAAAGTGTGGAGGCTACTGCAGAAGTTTCAAAGACGTTCAATGAGAAAATCAGAAAGTATTGTGATATGACACTTCTTTCATGTGCATATGCTGGAACCG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G28470.1 |
intron # | 15 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G28470.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: LOC_Os02g05340.1 (Oryza sativa), 3'ss of exon 17
gtgggcagccagtcatacttgattatttttcttgttcgtgtacttgatcg--ttatttccccgattattagtttta-acttgttc--caatatcga--gcagGAAAGTGTGGAGGCTACTGCAGAAGTTTCAAAGACGTTCAATGAGAAAATCAGAAAGTATTGTGATATGACACTTCTTTCATGTGCATATGCTGGAACCG
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-tatactat-agctgcctttgtttctaactgttgtttatggctttatgcagcccttttagataaatgtaccttttatgattgtttggcaatttccatttcagGAGAGTGTAGAGGCTACGGCAGAAGTTTCTAAAACATTTGATGAGAAGATAAGAAAGTACTGTGATGTAACACTTATGTCACTAGCATATGCTGGAACAG
upper sequence: AT4G28470.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA12G13410.1 (Glycine max), 3'ss of exon 17
-------------------------------------------gtgggcagccag--tcatacttgattatttttctt--gttcgtgtac-----ttgatcgttat----ttccccgattat-------tagttttaacttgttccaatatcga--------gcagGAAAGTGTGGAGGCTACTGCAGAAGTTTCAAAGACGTTCAATGAGAAAATCAGAAAGTATTGTGATATGACACTTCTTTCATGTGCATATGCTGGAACCG
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gtaaatagatgtctggcagtctatcatctctgtttttttaattatagattattttcttttcacctcattaatcttctttaatttctgaataacaattgatagtggtagggttctgctattgtgaaggtgtaatactcactctttacattgtgctttgttactgcagGACAGTGTTGAGGCAACTGCCGAAGTTTCAAAGACTTTCAATGAAAAAATTAGAAAGTATTGTGACATGACACTACTATCATGTGCCTATGCTGGAACTG
upper sequence: AT4G28470.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA06G44340.1 (Glycine max), 3'ss of exon 17
-----------------------------------------------------------gtgggcagccagtcatacttgatt-----atttttcttgttcgtgtacttgatcgttatttccccgattattagttttaacttgttccaatatcga--------gcagGAAAGTGTGGAGGCTACTGCAGAAGTTTCAAAGACGTTCAATGAGAAAATCAGAAAGTATTGTGATATGACACTTCTTTCATGTGCATATGCTGGAACCG
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gtaaacagatgtctggcaatctattgtctctgctttttgaatcatagattattttcttttcaattcattaatcttctttaatttctgaataacaattgatagtgagtagggttctgctattgttaaggtgtaatattcactctttacattgtgctttgttactgcagGACAGTGTTGAGGCAACTGCCGAAGTTTCAAAGACTTTCAATGAAAAAATTAGAAAGTACTGTGACATGACACTCTTATCATGTGCCTATGCTGGAACTG
upper sequence: AT4G28470.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: Vv12s0028g03130.t01 (Vitis vinifera), 3'ss of exon 17
-----------gtgg--gcagccagtcatacttgattatttttcttgttcgtgtacttgatcgttatttccccgattattagttttaacttgttccaatatcgagcagGAAAGTGTGGAGGCTACTGCAGAAGTTTCAAAGACGTTCAATGAGAAAATCAGAAAGTATTGTGATATGACACTTCTTTCATGTGCATATGCTGGAACCG
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tattatttactgtggtagaaaccatacaacatggaaaattttggaacttgaagttctaaataatt------ctaattatttctggaatccctatttggtgt--gacagGAAAGTGTGGAGGCCACTGCTGAAGTGTCAAAGACATTTAATGAAAAAATAAGAAAATATTGCGATATGACGTTGCTTTCTTGTGCATATGCTGGAACTGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|47828942|gb|CK118626.1|CK118626EST: TCACTCGTTTCTTGCCTCTTGGACTTGGTCTTTTGTACCTTGGCAAACAG GAAAGTGTGGAGGCTACTGCAGAAGTTTCAAAGACGTTCAATGAGAAAATC
genomic: TCACTCGTTTCTTGCCTCTTGGACTTGGTCTTTTGTACCTTGGCAAACAGgtgggcagcc ... tatcgagcagGAAAGTGTGGAGGCTACTGCAGAAGTTTCAAAGACGTTCAATGAGAAAATC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tacttgatcgttatttccccgattattagttttaacttgttccaatatcgagcagGAAAGTGTGGAGGCTACTGCAGAAGTTTCAAAGACGTTCAATGAGAAAATCAGAAAGTATTGTGATATGACACTTCTTTCATGTGCATATGCTGGAACCG
ttttaac putative branch site (score: 2)
attattagttttaact TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgggcagccagtcatacttgattatttttcttgttcgtgtacttgatcgttatttccccgattattagttttaacttgttccaatatcgagcagGAAAGTGTGGAGGCTACTGCAGAAGTTTCAAAGACGTTCAATGAGAAAATCAGAAAGTATTGTGATATGACACTTCTTTCATGTGCATATGCTGGAACCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA